SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction.

We present the jump-start simultaneous alignment and tree construction using hidden Markov models (SATCHMO-JS) web server for simultaneous estimation of protein multiple sequence alignments (MSAs) and phylogenetic trees. The server takes as input a set of sequences in FASTA format, and outputs a phylogenetic tree and MSA; these can be viewed online or downloaded from the website. SATCHMO-JS is an extension of the SATCHMO algorithm, and employs a divide-and-conquer strategy to jump-start SATCHMO at a higher point in the phylogenetic tree, reducing the computational complexity of the progressive all-versus-all HMM-HMM scoring and alignment. Results on a benchmark dataset of 983 structurally aligned pairs from the PREFAB benchmark dataset show that SATCHMO-JS provides a statistically significant improvement in alignment accuracy over MUSCLE, Multiple Alignment using Fast Fourier Transform (MAFFT), ClustalW and the original SATCHMO algorithm. The SATCHMO-JS webserver is available at http://phylogenomics.berkeley.edu/satchmo-js. The datasets used in these experiments are available for download at http://phylogenomics.berkeley.edu/satchmo-js/supplementary/

Development and testing of an assessment tool for integrated learning

Objective: Development of integrated questions for undergraduate medical students and assessing students’ capability to retain and apply basic concepts in an integrated way. Method: Multiple choice questions, attempting to probe understanding and application of different concepts, affiliated with different subjects and topics, were developed. As a pilot these were administered to the students of third year and final year at the end of their certifying examinations as a mock test. The following year these questions were introduced in the continuous assessments and subsequently the certifying examinations (in third year) as 33% of the whole examination. Difficult indices, item analysis and internal consistency (alpha) were calculated for all the questions. Results: The difficulty indices of integrated questions indicated that students found the integrated questions difficult. Conclusion: There was a significant change of distribution in terms of scoring for the integrated questions. Students’ power to integrate showed reliable improvement when tested in the certifying examinations (JPMA 51:384,2001)

Biomechanical properties of bone in a mouse model of Rett syndrome

Rett syndrome (RTT) is an X-linked genetic disorder and a major cause of intellectual disability in girls. Mutations in the methyl-CpG binding protein 2 (<i>MECP2</i>) gene are the primary cause of the disorder. Despite the dominant neurological phenotypes, <i>MECP2</i> is expressed ubiquitously throughout the body and a number of peripheral phenotypes such as scoliosis, reduced bone mineral density and skeletal fractures are also common and important clinical features of the disorder. In order to explore whether MeCP2 protein deficiency results in altered structural and functional properties of bone and to test the potential reversibility of any defects, we have conducted a series of histological, imaging and biomechanical tests of bone in a functional knockout mouse model of RTT. Both hemizygous <i>Mecp2</i><sup>stop/y</sup> male mice in which <i>Mecp2</i> is silenced in all cells and female <i>Mecp2</i><sup>stop/+</sup> mice in which <i>Mecp2</i> is silenced in ~ 50% of cells as a consequence of random X-chromosome inactivation, revealed significant reductions in cortical bone stiffness, microhardness and tensile modulus. Microstructural analysis also revealed alterations in both cortical and cancellous femoral bone between wild-type and MeCP2-deficient mice. Furthermore, unsilencing of <i>Mecp2</i> in adult mice cre-mediated stop cassette deletion resulted in a restoration of biomechanical properties (stiffness, microhardness) towards wild-type levels. These results show that MeCP2-deficiency results in overt, but potentially reversible, alterations in the biomechanical integrity of bone and highlights the importance of targeting skeletal phenotypes in considering the development of pharmacological and gene-based therapies

The Geochemical Distribution and Assessment of Heavy metals Pollutions in Soil Sediment of Chamchamal City-Sulaimanya Governorate / NortherEastern Iraq.

The current study aims at the geochemical distribution of heavy elements in soil sediments.It assesses environmental pollution using pollution index and potential health hazards in the city of Chamchamal  northeastern Iraq. Twenty-one samples of soil sediments were collected in the area of residential, commercial and industrial areas in mid-July 2017. Heavy metals (As, Cu, Cr, Cd, Co, Fe, Mn, Mo, Ni, Pb, Zn) were analyzed using ICP-MS. The results showed that arsenic, chromium, cadmium, cobalt, manganese and nickel were the highest concentration in residential areas.While molybdenum and lead were higher in commercial areas, wheras copper, iron and zinc recorded the highest concentration in industrial areas. The results of pollution indicators (Igeo) showed that the  arsenic was the  (Moderately contaminated), The values of the (EF) index of the arsenic  are (Significant enrichment), the cadmium and nickel were (moderate enrichment), and the values of Cdeg showed that some of  samples are (Contamination Moderate) wheras the rest of the sites are considered (Contaminated) by  heavy metals studied. The PRI values indicated that some models were of (Riskable) and others (Very High Risk). key words: chemchmal area, heavy metal, pollution , health ris

Verrucopapillary Lesions of the Oral Cavity: A Review

Verrucopapillary lesions are a spectrum of benign, potentially malignant and malignant lesions of the oral mucosa which usually are misdiagnosed. They pose a great diagnostic challenge mainly due to confusing terminology and also due to similar clinical and histopathological features which often makes these lesions indistinguishable from one another. The human papilloma virus (HPV) plays a important role in the pathogenesis of majority of these lesions. This review aims to summarize and highlight the key clinical and histopathological features of these lesions, and also provides a diagnostic approach to these entities

Role of labour admission test in predicting pregnancy outcome in low-risk cases

Background: The present study was carried out to determine the role of labour admission test (LAT) in detecting fetal hypoxia in labour and to correlate the findings of the test with perinatal outcome in low-risk cases.Methods: In this study 150 low risk pregnant term women were subjected to LAT and classified according to NICE 2017 guidelines. Pregnancy outcome in terms of need for operative delivery and neonatal status at birth were noted. Data was analysed statistically by Chi-square test.Results: The LAT was normal in 78.67%, suspicious in 17.33% and pathological in 4%. Operative delivery for fetal distress was observed in 18.75% of normal group, in 50% of suspicious group and in 100% of pathological group. The incidence of meconium-stained liquor was significantly high in pathological (50%) and suspicious group (19.23%). The incidence of low 5-minute Apgar score was significantly high in pathological LAT group (33.33%) as compared to suspicious (7.69%) and normal LAT groups (2.54%). Admission to neonatal intensive care unit (NICU) was significantly high in pathological test group (50%). LAT in this study showed 48.15% sensitivity, 96.75% specificity and 76.47% positive predictive value as a screening tool for predicting fetal distress in low-risk patients suggesting that a normal LAT in early labour is an indicator of good pregnancy outcome.Conclusions: LAT is an effective, non-invasive screening method with good specificity to detect fetal distress in low-risk woman and helps to plan management accordingly to improve pregnancy outcome

Pengembangan Catu Daya Presisi Display Digital Untuk Praktikum Fisika Listrik Dinamis

This study aims to generate power supply precision instrument digital display a valid and practical for students of physics 3rd semester of the school year 2014/2015. This research includes development research (research development) of the power supply circuit that has been common there are some drawbacks, namely, the output of output that does not fit, there is still AC voltage on the output value, the output voltage is unstable, so that the results of the lab basic physics 2 be not in accordance with the results of the theory. The addition of the diode bridge circuit helps perfect output voltage into DC, the capacitors in the circuit capacity was raised as a reliever ripple or ripples form to obtain a stable DC voltage value, for a voltage stabilizer is also used IC9815 surge protector. Limited trial conducted in STAIN Batusangakar to 26 students. Based on the results of data analysis has been carried out can be summarized as follows: (1) The results of the validation tool precision power supply digital display is very valid. (2) The results of trials carried out showed that the practicalities have met the criteria that can be used and implemented in a lab with practicality very practical value

Teleparallel Killing Vectors of Spherically Symmetric Spacetimes

In this paper, Killing vectors of spherically spacetimes have been evaluated in the context of teleparallel theory of gravitation. Further, we investigate the Killing vectors of the Friedmann metrics. It is found that for static spherically spacetimes the number of Killing vectors turn out to be \emph{seven} while for the Friedmann models, we obtain \emph{six} teleparallel Killing vectors. The results are then compared with those of General Relativity. We conclude that both of these descriptions of gravity do not provide the consistent results in general. However, these results may coincide under certain conditions for a particular spacetime.Comment: 14 pages, accepted for publication in Communications in Theoretical Physic

Polymer Bound Elastase Inhibitors

Pharmaceutical compositions and methods of inhibiting the enzyme elastase and increasing the biological half-life and/or potency in terms of inhibitory activity of the enzyme elastase of peptide compounds is achieved by use of a polymer of the formula P--(L--R)q wherein P is a polymer containing at least one unit of the formula (An Bn) wherein An Bn is substantially nonbiodegradable, and has an average molecular weight of about 1,000 to 5,000 daltons, L is a covalent bond or a linker group and R is a peptide

Design and construction Optically Gas Laser

In this work the design and construction of a flash photolysis pulsed HCl laser was presented. The parameters of the pumping source and discharge current density was obtained, which sufficient to shift the flash lamp spectrum towards uv portion of spectrum. The maximum pulse laser energy parameters was measured. Total pressure and ratio of active gases to optimized the output pulse energy were measured , where at 125 mbar of total pressure and 1:7:14 Cl2:H2: He ratio, the laser energy was measured to be 200 mJ at pumping four flash lamps energy in the order of 6400J .The resonator consists of copper a near hemispherical mirror with the radius of curvature 3m coated by gold and reflectivity 98%,the output coupler sapphire mirror of 63% reflectivity . Total efficiency of the system was measured to be 0.0125%